Comparison between surface and bead-based MALDI profiling technologies using a single bioinformatics algorithm

In this manuscript, we compared serum profiles obtained with two related technologies, SELDI-TOF and Clinprot, using a single bioinformatic algorithm. These two approaches rely on mass spectrometry to detect proteins and peptides initially selected by binding to various chromatographic matrices. They are proposed by two different companies, and they are competing for being the reference in high throughput serum profiling for clinical proteomics. This independent evaluation of these two technologies put the light on some of their differences, suggests that they address different proteome fractions and, thus, could be complementary. Taken together, our data could contribute to the parameters relevant for the choice of one technology or the other.